9JF4 | pdb_00009jf4

cryo-EM structure of Neuromedin B receptor in complex with PD168368

• PDB DOI: https://doi.org/10.2210/pdb9JF4/pdb
• EM Map EMD-61427: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2024-09-03 Released: 2025-07-09 
• Deposition Author(s): Gao, K., Zhang, X., Liu, X.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

cryo-EM structure of Neuromedin B receptor in complex with PD168368

Gao, K., Zhang, X., Liu, X.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 57.47 kDa 
• Atom Count: 2,782 
• Modeled Residue Count: 392 
• Deposited Residue Count: 520 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neuromedin-B receptor,de novo design protein	A	520	Homo sapiens	Mutation(s): 0  Gene Names: NMBR
UniProt & NIH Common Fund Data Resources
Find proteins for P28336 (Homo sapiens) Explore P28336  Go to UniProtKB:  P28336
PHAROS:  P28336 GTEx:  ENSG00000135577

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1D63 (Subject of Investigation/LOI)	B [auth A]	(2~{S})-3-(1~{H}-indol-3-yl)-2-methyl-2-[(4-nitrophenyl)carbamoylamino]-~{N}-[(1-pyridin-2-ylcyclohexyl)methyl]propanamide C31 H34 N6 O4 AFDXUTWMFMAQJO-PMERELPUSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.60 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-09 
Deposition Author(s): Gao, K., Zhang, X., Liu, X.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	81974236

Revision History  

• Version 1.0: 2025-07-09
  Type: Initial release